The Equestrian Civil War
by xxxRavensClawxxx
Summary: Three years after Twilight Sparkle was put to sleep by a mercenary, she wakes up to a new and different Equestria where Princess Luna and Princess Celestia have split off to make seperate sides who wage war in a final battle for supremacy. But can Twilight choose the right side?
1. Chapter 1

**Audience! K, so I recently became a bronie, a boy over the age of 8 who watches My Little Pony: Friendship is Magic! (Awesome Show!) Anyway, this is an idea of mine. Summary:**

**When Twilight Sparkle and Spike are put to sleep by a mysterious figure, they wake up 3 years later to find Equestria in Civil War. The princesses Luna and Celestia have split apart to create the United Confederation of the Moon, and the Celestial Empire of the Sun. Siding with Princess Celestia, the young unicorn faces the UCM with bravery. Little does she know that the faction she fights for isn't as pure as it seems...**

**Enjoy!**

**Rated +13 for scenes of torture and war.**

**Chapter 1: Thickening Shadows**

"Rainbow Dash, where's my brush?" Twilight Sparkle called to her best friend. She frantically tried to push the top of the bag shut, but to no avail. The pile of books wouldn't fit, no matter what magic she could muster from her horn.

"Here it is, Twilight." The cyan pegasus mumbled around the sparkly brush in her mouth. Twilight sighed in relief as she added that to the rapidly growing pile in her bag.

"Here Twilight, you can borrow my bags." A quiet voice said from behind her. Twilight and Rainbow Dash turned to see Fluttershy, holding the said bags on her back.

"Thanks Fluttershy, but I couldn't. You'll need them here." Twilight smiled at her animal-loving friend. The yellowish filly stamped at the ground and sighed a little. She suddenly fell over as Applejack pushed through, hauling a sack of food behind her.

"Giddy-up, girls! Applejack is here with the snacks!" She neighed.

"And me too!" A higher voice called. Pinkie Pie bounced in with a bag of sweets behind her. Before the purple unicorn could say anything, the sacks were tied to her bags. She grumbled as she guessed how heavy the bags were now.

Another young mare trotted in, with flowing purple curls and a white coat.

"Come on Rarity, not you too!" Twilight began, but Rarity was already putting outfits into the bags.

"We don't want you looking like a ruffian while you're out there, do we?" Rarity asked as she piled the clothes into the bags before closing it, which perplexed the purple-maned unicorn to no end after she had tried to do that for over an hour.

They loaded the bags onto Twilight Sparkle's back, almost crushing her in the event. They changed tactics and loaded the bags onto a cart borrowed from Fluttershy. That was when the purple-and-green dragon Spike walked out, carrying a bag of food on his back.

As Twilight prepared to embark, a golden chariot flew down from the sky, pulled by armored stallions. The flowing rainbow-mane of Princess Celestia was seen, with the equally flowing dark-blue mane of Princess Luna. Everypony bowed to the royal sisters, who stepped off of the chariot.

"Twilight Sparkle, my faithful student. Are you ready to embark on this quest?" Princess Celestia asked the purple unicorn.

"Yes, Princess. I won't let you down!" Twilight answered faithfully. Princess Luna stepped forward, her face set as grim.

"On most occasions, we would send your friends with you, but they will be needed here. We have full confidence in you that you will do just as well alone as you would together." The young mare gulped at the responsibility she had.

"On that note, good luck." Celestia said in farewell. Twilight nodded and began the long journey to the other side of the Everfree Forest.

Spike yawned. It had taken four days, and many animals had frightened them, but they were finally in a far-off land on the other side of the Everfree Forest called Coltfield. The ponies there seemed unfriendly to the Equestrians, for Coltfield was outside of Celestia's borders.

"So, Twilight... what are we doing here again?" The purple-and-green dragon asked his unicorn companion.

"The Princesses said that the people here aren't totally friendly to Equestrians. I have to check for any signs of possible attack." Twilight explained. Spike gulped at the fact of possible danger before snuggling into Twilight Sparkle's mane.

They walked through the little town. It was not dissimilar to Ponyville, except that there were a lot of glares in the direction of the magic wielding unicorn. She walked into the largest building: The City Hall.

Twilight walked into the main room, and after some grudgingly-given information, walked into the Mayor's office.

The mayor was a large pony with gray hair. His mane was black as midnight, and his body was tall. He was intimidating.

The mayor turned around and spotted Twilight.

"What do you want?" He sneered. Twilight took no notice.

"I'm Twilight Sparkle, and I was told to stay here in Coltfield for a few days. I sent a message requesting lodgings for a month." She explained. The mayor grunted and waved another pony forward.

This pony was hooded and cloaked, so Twilight couldn't see his face. He was big, almost as big as the Mayor. She also noticed a slight bump in his hood - a horn?

"My assistant here will take you to your lodgings. He will keep you safe." Twilight thought she detected a slight change in his voice, but took no notice of it. She followed the cloaked colt as they walked through the town. They ended up in front of a run-down cottage. The windows were all boarded up, and Twilight couldn't see any furniture inside. They entered the living room, and the cloaked pony shut and locked the door.

"Uh, may I ask what you're doing?" The stallion didn't answer. He pulled a chair out from the shadows of the room.

"Sit." He ordered. Twilight sat. Spike sat on the seat with her.

"What's going on? Why are you doing this?" the purple unicorn asked with fear in her voice. He pulled off his cloak, and she saw his face at last.

His coat was gray, and he had a brown and black mane. He removed his sunglasses, revealing his blood-red eyes that gleamed like fire. He was a unicorn, but his horn was shattered near the base.

"You are a smart one. Too smart. You may interefere with my employer's plans. Therefore, you must be removed. And I'm just the stallion for the job." She suddenly realized he meant to kill her, and she struggled against the ropes that had somehow tied themselves to her.

"Don't! The princesses will find out, and you'll be sorry." she desperately threatened. He laughed, a cold, cruel sound.

"So long, unicorn." he cackled one last time, then charged his horn and aimed it at Spike and Twilight Sparkle. There was a brilliant flash, then silence. Darkness enveloped the purple filly, and she slipped into the cold embrace. The last thing she saw before total unconcsiousness was a vision of her friends, calling out to her. Then they were gone, along with all life signs in her body.

**What on Earth? Twilight and Spike are supposedly killed by a unicorn mercenary, and she somehow could interfere with his employer's plans? Next time, Twilight wakes up, but to a whole new Equestria. Till next time! Quickly, this is shorter than most chapters will be.**


	2. Chapter 2

**Alright! So last chapter, Twilight and Spike were ambushed by a unicorn that was employed to take her out. She is dead now... or is she? We tune in as she wakes up...**

**Really quick, ponies do use weapons in this. I know they wouldn't normally, but why be subtle? My excuse is that in three years, the princesses rediscovered that if you infuse magic and metal in a certain way, they new weapon can shoot pellets of metal with deadly results.**

**Chapter 2: A Whole New World**

The difference between life and death blurred together. Memories became past lives, and life became myths. Twilight could see nothing but darkness, almost losing all remembrance of her friends in Ponyville. She assumed that this was death, and that she must have done something wrong in life. Then she heard a voice.

"Twilight! Get up!" Spike was calling. She came out of her vision of blackness to see her assistant shaking her in an attempt to get her up. The purple unicorn groaned as she stood up, shaking out her stiff limbs. Looking around, she realized she wasn't in her Library anymore.

"Spike, where are we?" Then memory flooded back, and she remembered the mercenary. Without a word, Spike put Twilight Sparkle's saddle bags on her before climbing onto her back.

They walked outside, surprised to see all the windows and the door all boarded up and chained. With a little magic, the chains and planks fell off the door, and they entered the yard of the old house.

"This is Coltsfield... but it's older and rundown!" the purple and green dragon exclaimed. The unicorn nodded and walked to the path she had taken to enter the town.

"Come on, Spike. This isn't normal, and I mean to find out what happened." Spike nodded determinedly. Taking a deep breath, they began the long trip back to the Equestria they knew and loved... or so they thought...

The duo trekked through the Everfree Forest, noting the odd lack of animals. No Timberwolves, no phoenixes, not even an owl. Just as they came to where Zecora's hut was, they stumbled into a hole. Except it was more than a hole.

"What the hay..." Twilight whispered.

All around them were charred and snapped tree trunks, burned to the ground. Where Zecora's house should have been, there was a black crater in it's place. Only a shard of one of her masks was left, and that was burned beyond recognition. Twilight didn't cry, she didn't scream. All she could do was slump to the ground.

"What did this?" She whispered. Spike didn't answer. He had no answer to give. It was a good hour before Twilight finally got up. She put Spike on her back and proceeded to walk to her home, not knowing she was being watched.

"Freeze." said a voice behind her. She turned to see a muzzle of a pistol aimed at her. Earth-Ponies melted out from the trees, each holding a weapon. Their faces were hidden by a mask in the shape of a skull. The pistol belonged to a unicorn who was presumably the leader.

"Who are you? A Confederate spy?" He growled. She shook her head in a confused way.

"What Confederate? I was sent out of Equestria on a mission by Princess Celestia, and I was just going back to report..."

"A likely story." he spit. "We're taking you to the Sarge." He kicked her and she got up with a yelp. Surrounded by armed ponies, she had no choice but to follow them. They finally came out of the forest, but in front of a stone fortress rather than Ponyville. The unicorn angrily went up to a pegasus who was cleaning a machine gun.

"Topaz, where the hay is the sarge?" He said angrily. The pegasus blew a stray piece of his green mane out of his eyes.

"Sarge said he was urgently needed in Canterlot. He's sending a carrier back for you, Don." As he said this, a flap of wings was heard. Twilight and Spike looked up to see a large chariot pulled by at least 6 pegasi landing in front of them. A flap rolled down to serve as a ramp for the squad and their prisoners.

"Get on." One pony grunted, pushing the purple unicorn and her dragon friend up the ramp and onto a seat. The rest of the ponies got on, with the unicorn sitting closest to Twilight Sparkle. The ramp closed, and they took flight once more.

As they flew through the sky, Twilight thought about what she now learned. Obviously, she had been asleep for some time. There were new modes of transportation that had been made. And this unicorn "Don" that now sat next to her wasn't a leader. There must be another, but who?

After exhaustion from a long walk, Twilight and Spike both fell into a light sleep.

Twilight is suddenly woken up, but surprisingly is being gently shaken. She looks up into the gentle aqua-green eyes of an Earth-Pony. He had an assault rifle slung across his back. A mask hid his face, and he had a curly brown mane.

"Hey, sorry to wake you, but we have to blindfold you again. If I could have my way, you would be allowed to walk free, but it's Don's orders." He smiled apologetically, and put a blindfold on her, but not as tightly as she expected.

After he secured it, she felt herself being led off the chariot, and then she stopped paying attention. After what seemed like hours, she finally was unveiled, revealing the giant doors leading to the Princess' throne room.

_I'm in Canterlot! _She realized, then thought about something frightening. These ponies have loaded weaponry that hasn't been used since the dark times! Maybe the princesses have been overthrown... or even worse, killed! Her thoughts were interrupted when the doors swung open.

Twilight and Spike, no longer caring what happened, walked in. What they found surprised them. In front of her was Princess Celestia and Shining Armor.

"Princess!" She was interrupted by a smack on the head from the unicorn behind her, which left a nasty bump. _That'll smart later._ He looked up Shining Armor.

"Sarge, we found this one skulking around the old hut. Confederate scum." He spat. Armor looked over and a grin took over his face.

"Twily! Oh my gosh, I was sure you were dead! Thank Celestia you're okay!" He looked at the unicorn. "Release my sister." Don immediately released Twilight's restraints, apologizing quickly and repeatedly. The unicorn didn't forgive him, but she didn't scold him either. Right now, she was just in shock.

"Twily! Oh Celestia, I thought I'd never see you again!" Shining Armor said as he hugged Twilight and kissed her head over and over again. She realized he was crying, his tears dripping into her fur and soaking it. She realized that she too was crying.

Then she saw her mentor. The Alicorn of the Sun, Princess Celestia. She seemed to scowl for a moment, then slowly smiled. Not with her mouth, but with her eyes. _Probably my mind playing tricks on me. _Twilight thought, brushing off the scowl.

"Twilight Sparkle, my faithful student. We were all sure you were dead."

"What?" She pushed Shining Armor off of her. "Why would I be dead? What in Equestria is going on here? There are soldier ponies with weaponry from the dark ages! And Zecora's hut is just a crater!"

"Yes, much has changed in three years."

"Three years?" Spike asked Twilight quietly. "If that's true, we just slept without drinking and eating for all this time, and somehow we're still alive."

"Tell me what happened. Last I saw you, I had sent you to Coltsfield." Princess Celestia and Twilight Sparkle walked for hours, and the unicorn told her mentor about what had gone on after she had left all that time ago. Finally, she was done.

"Know, could you please explain what happened here while I was gone?" Celestia nodded and began walking up the staircase. Twilight knew that it led to the Citadel, the tallest of the towers in Canterlot. The white alicorn signaled for her student to follow her.

They walked for several minutes, finally coming to a balcony. That balcony gave anypony who was on it a view of all of Equestria. Celestia gazed across her country with a look of pride. Then she spoke.

"Some develop jealousy, and some are born with it. Most control it, but some choose otherwise. Jealousy is what can split kingdoms and shatter bonds. And it has done so here."

"What do you mean?" Twilight asked.

"These tidings are not good, my faithful student."

"Tell me." Twilight insisted. Celestia sighed and stared right into the unicorn's purple eyes.

"We are at war."

Twilight had guessed as much, but she had hoped that it had been otherwise. Now nothing could hold back the wave of shock that now overcame her. When she had recovered, she anxiously said what was eating at her mind.

"Who are you fighting against?"

"My sister, Princess Luna." Celestia replied, with anger hot in her voice. "She tried to take back the throne for herself and only herself. When I retaliated, she snuck off to form an army to oppose us. Now we are at war, the First Equestrian Civil War." Twilight was even more shocked at this. But one more question egged her on.

"Where are my friends?" Celestia looked away for a few minutes, and then looked back with tears in her royal eyes.

"Your friends are…"

"My friends are WHAT?!" Twilight shouted.

"Your friends are all… dead."

**Chapter 2 is done! I think this story can make it well to 50 chapters without me trying, so there is A LOT more to come! Till next time!**


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